On-loan striker Ade Akinbiyi confirmed Stoke's first division status as Reading, already assured of a play-off place, posed little threat.
City, favourites for relegation two months ago, completed a notable Houdini act by winning half of their last 12 games and keeping eight clean sheets in the process.
As it happened, Brighton's failure to win at Grimsby made this result academic, leaving Stoke five points clear of the bottom three.
Stoke boss Tony Pulis, despite pre-match forecasts of all out attack, selected a 4-5-1 formation to match Reading man for man.
But City did create what little excitement there was in the first half as Lewis Neal tested Marcus Hahnemann.
The all-important goal arrived ten minutes after the interval, with Neal the provider with a pin-point cross for hero Akinbiyi.
Neal looked to be chasing a lost cause towards the byline, but hooked a superb near-post delivery which Akinbiyi finished with a flashing header from point-blank range.
Reading did pose more of a threat in the latter stages, with Steven Sidwell inches off target from 20 yards, before Stoke's celebrations began.
After the game Pulis insisted an FA Cup run which netted the club in excess of £250,000, had played a major part in helping Stoke escaping the drop.
"I was able to bring in Akinbiyi, Crossley, Warhurst, and Williams and they have all done their bit," he said.
"Ade had a bad time at Leicester but I signed him for Gillingham from Norwich as a kid and I have always rated him.
"He's only been half fit because of hamstring problems but he scored us a couple of very important goals.
"We were six points behind Brighton at one point and an 11-point turnaround represents a remarkable achievement for everyone at the club." Reading boss Alan Pardew, whose side face Wolves in the play-offs, said: "We tried to talk the players up for the game, but Stoke had that bit of edge which swung it for them.
"I don't think my team would have played like that if it was a play-off game."